|
| Status |
Public on Jul 09, 2019 |
| Title |
MDAMB231_BRD4_100nMJQ1_48h_rDNA |
| Sample type |
SRA |
| |
|
| Source name |
MDAMB231 breast carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDAMB231
treatment: 100nMJQ1 48h rDNA
culture media: DMEM/F12 1:1 supplemented with 5% FBS, 5 ug/ml insulin, 1 ug/ml hydrocortisone
library preparation kit: KAPA Hyper Prep
chip antibody: BRD4 Bethyl Laboratories A301-985A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies.
All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MDAMB231_rDNA_250bp_bins.xlsx
|
| Data processing |
Reads were aligned to hg19 or to a single copy of the ribosomal DNA repeat (GenBank: U13369.1) using Bowtie v1.1.2 with parameters -v 2 -m 1.
Genome_build: hg19
Supplementary_files_format_and_content: The following processing steps were performed to generate peakclassification files: Calculating read density: The density of reads in each region was normalized to the total number of million mapped reads producing read density in units of reads per million mapped reads (rpm). The read density of the input chromatin was subtracted from the ChIP read density for normalization. Peak calling: We used a combination of two algorithms, MACS v1.4.2 and HMCan v1.21, to define enriched regions. We used HMCan to call peaks in regions of high CNV, defined as regions of size > 50 kb where no MACS peaks are called, and have read coverage that is >3 times the average read coverage. Peaks within 12.5 kb of each other were stitched as described in Loven et al. 2013 Cell 153. We used default settings for MACS, and HMCan was run with narrow peak calling configuration file with no blacklisted regions. Peak genic classification: A peak region was classified on the basis of its location with respect to GRCh37/hg19 gene annotations. If the region was +/- 5 kb of any transcription start site, it was classified as a promoter peak. If it was within -5kb to -200kb of any transcriptional start site, it was classified as a 5' enhancer peak. If the peak overlapped the gene boundary, and was not classified as a promoter or enhancer peak, it was classified as either a genebody_exon or genebody_intron peak. If the peak resided within 0 to +200kb from the 3'-most exon, and did not fulfill the criteria for the above classifications, it was classified as a 3' enhancer. All remaining peaks were designated as "other".
|
| |
|
| Submission date |
Jul 10, 2018 |
| Last update date |
Jul 09, 2019 |
| Contact name |
Gary L Johnson |
| E-mail(s) |
glj@med.unc.edu
|
| Phone |
919-843-3107
|
| Organization name |
UNC Chapel Hill SOM
|
| Department |
Pharmacology
|
| Lab |
Gary L. Johnson
|
| Street address |
120 Mason Farm Road Genetic Medicine Building CB#7365
|
| City |
Chapel Hill |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE116879 |
Response of triple negative breast cancer to BAZ2A/B inhibition and BET bromodomain inhibition alone and in combination (ChIPseq) |
| GSE116919 |
Response of triple negative breast cancer to BAZ2A/B inhibition and BET bromodomain inhibition alone and in combination |
|
| Relations |
| BioSample |
SAMN09638163 |
| SRA |
SRX4377557 |
